Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped21888291.375%
Wrongly Mapped206568.623%
Not Mapped40.002%
Total239542100.0%
Read Failure Statistics
Not mapped10.0%
Missing in mapper output30.001%
Mapped to wrong chromosome114414.776%
Mapped to wrong position92153.847%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment27
Secondary Alignments0
F-Measure0.954900
Precision0.913800
Recall1.000000
Timing
Raw Mapping Time330.980s
Effective Mapping Time330.809s
Effective Init Time0.171s
Effective Time MeasureCPU
Mapping Time (Wall)173.253s
Mapping Time (CPU)330.980s
Mapping Time (CPU User)330.067s
Mapping Time (CPU System)0.913s
Init Time (Wall)0.208s
Init Time (CPU)0.171s
Init Time (CPU User)0.009s
Init Time (CPU System)0.162s
Additional Information
Mapper Memory Usage504 MB
Total Test Runtime (Wall)199.712s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247272000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.175 sec; CPU: 0.139 sec
systime0.132979
time0.178615093231
usrtime0.008998
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247276000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.204 sec; CPU: 0.168 sec
systime0.161975
time0.207754135132
usrtime0.008998
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory504140000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 239542 sequences/pairs (35931300 bp) ...
[bsw2_stat] infer the insert size distribution from 24943 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (176, 198, 220)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 308)
[bsw2_stat] mean and std.dev: (200.07, 29.55)
[bsw2_stat] low and high boundaries for proper pairs: (150, 352)
[bsw2_pair] #fixed=610, #rescued=8, #moved=7
[bsw2_stat] infer the insert size distribution from 24901 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (176, 198, 220)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 308)
[bsw2_stat] mean and std.dev: (199.96, 29.55)
[bsw2_stat] low and high boundaries for proper pairs: (150, 352)
[bsw2_pair] #fixed=613, #rescued=7, #moved=12
[bsw2_stat] infer the insert size distribution from 24942 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (176, 198, 220)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 308)
[bsw2_stat] mean and std.dev: (200.08, 29.48)
[bsw2_stat] low and high boundaries for proper pairs: (150, 352)
[bsw2_pair] #fixed=554, #rescued=13, #moved=10
[bsw2_stat] infer the insert size distribution from 25077 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 198, 220)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 306)
[bsw2_stat] mean and std.dev: (200.45, 29.63)
[bsw2_stat] low and high boundaries for proper pairs: (150, 349)
[bsw2_pair] #fixed=590, #rescued=12, #moved=12
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 173.221 sec; CPU: 330.968 sec
systime0.912861
time173.253216028
usrtime330.066822
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae